[gmx-users] number of water molecules affects the PMF
Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules as a variable. I calculated the error by dividing the whole data to 4, and calculated the standard deviation between the 4 sets, and divided the result by sqrt (3). For the Xavier's suggestion: I think I should wait a little, at least until having the same length of trajectory for the two sets. Thanks -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] number of water molecules affects the PMF
On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote: Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules as a variable. I calculated the error by dividing the whole data to 4, and calculated the standard deviation between the 4 sets, and divided the result by sqrt (3). For the Xavier's suggestion: I think I should wait a little, at least until having the same length of trajectory for the two sets. Here we go! You are probably not converged! How long did you simulate? Thanks -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] number of water molecules affects the PMF
Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and then I integrated the mean force curve to get the PMF. In order to test how big the effect of the number of water molecules on the calculated PMF I performed two sets of simulations which differed from each other in terms of only the number of water molecules. I used 9000 water molecules in one set, and 7000 in the other. The overall PMF for the latter was steeper than the former, as I expected before. However, the minimum point for the former was around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think that the difference should not be that much since there is not a big difference between the number of water molecules between the two sets. I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] number of water molecules affects the PMF
On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote: Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and then I integrated the mean force curve to get the PMF. In order to test how big the effect of the number of water molecules on the calculated PMF I performed two sets of simulations which differed from each other in terms of only the number of water molecules. I used 9000 water molecules in one set, and 7000 in the other. The overall PMF for the latter was steeper than the former, as I expected before. However, the minimum point for the former was around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think that the difference should not be that much since there is not a big difference between the number of water molecules between the two sets. Could it be that the difference is within the error ? What happens if you cut your data of each simulation in two pieces? In other words are you converged? I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] number of water molecules affects the PMF
It depends on how you generated your error bars and how different your two setups were other than different numbers of water. Xavier's suggestion to split the sampling in half and report each half to the list remains an important piece of data for us to have. Also, please don't reply to the entire digest. Instead, cut and paste the relevant text. Chris. -- original message -- Hi Xavier, Ok, it would be better to talk with the average values together with the corresponding error bars. For the system having smaller number of water molecules the minimum of the PMF was around -4.31+-0.97 kJ/mol, and for the other system it was around -1.75+-1.05 kJ/mol. Therefore, the difference is significant. Regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
